This application claims the priority of Korean Patent Application No. 10-2003-0097806, filed on Dec. 26, 2003, in the Korean Intellectual Property Office, the disclosure of which is incorporated herein in its entirety by reference.
1. Field of the Invention
The present invention relates to a robust method of identifying whether a target nucleic acid is a wild type or a mutant type using a DNA chip and a DNA chip used therein.
2. Description of the Related Art
The most common genotyping method is to identify sequences using sequencing machine. This method is accurate but is unsuitable for genotyping a number of samples simultaneously and leads to a low yield.
Recent disclosures of DNA chips that can simultaneously identify various genotypes at different positions, such as U.S. Pat. Nos. 6,027,880 and 6,300,063, are attracting a lot of interest. The DNA chips disclosed in the patents utilize tiled arrays of from 9 to 25-mer oligonucleotide probes at non-mutation sites and A, C, G, and T at mutation sites. Since all possible base combinations are used for a tiled array of probes mobilized at or close to mutation sites, the number of required probes increases four times whenever one more tiled array site is required.
However, such a tiled array includes redundant probes for an identified target nucleic acid. In addition, the tiled array method cannot be applied to detect mutations, for example, by insertion or deletion. Since a tiled array includes numerous probes having similar sequences and a fixed length, it is difficult to accurately analyze the results of genotyping a particular locus using such a tiled array, and then, the manufacturing costs of DNA chips rise. For example, if the hybridization intensity of a wild-perfect match probe or a mutant-perfect match probe is lower than the hybridization intensity of the other mismatch probes, a genotyping error occurs and thus, it is not possible to prove a cross-hybridization effect. Also, the fixed length of the probes in the tiled array hinders the optimal hybridization with a particular nucleic acid.